Merge branch 'master' into update-cambridge-config

Author: RaqManzano

conf/bluebear.config

@@ -19,7 +19,7 @@ env.TMPDIR = "/scratch/${System.getenv('USER')}"
 // Enable Singularity (via Apptainer) for all processes
 singularity {
     enabled    = true
-    autoMount  = true
+    autoMounts = true
     runOptions = "-B /scratch/${System.getenv('USER')}"
 }
 

conf/embl_hd.config

@@ -15,18 +15,19 @@ docker {
 
 apptainer {
     autoMounts = true
-    pullTimeout = "3 hours"                // the default is 20 minutes and fails with large images
+    pullTimeout = "3h"                // the default is 20 minutes and fails with large images
     envWhitelist = 'CUDA_VISIBLE_DEVICES'  // allow the bounding of GPU visible device variable into the containers
     libraryDir = '/cvmfs/singularity.galaxyproject.org/all/'
 }
 
 singularity {
     autoMounts = true
-    pullTimeout = "3 hours"
+    pullTimeout = "3h"
     envWhitelist = 'CUDA_VISIBLE_DEVICES'
 }
 
 process {
+    executor = 'slurm'
     maxRetries = 3
     errorStrategy = { task.attempt<3 ? 'retry' : 'ignore' }
     cache = 'lenient'
@@ -53,5 +54,5 @@ executor {
     submitRateLimit = "10/1sec"
     pollInterval = '10sec'
     exitReadTimeout = "5 min"
-    retry.reason = "*"
+    retry.reason = ".*"
 }

conf/kaust.config

@@ -8,7 +8,7 @@ params {
 }
 
 // Load genome resources and assets hosted by the Bioinformatics team on IBEX cluster
-includeConfig 'https://raw.githubusercontent.com/bioinfo-kaust/references/refs/heads/main/configs/genomes.config'
+includeConfig (!System.getenv('NXF_OFFLINE') ? "https://raw.githubusercontent.com/bioinfo-kaust/references/refs/heads/main/configs/genomes.config" : "/dev/null")
 
 singularity {
     enabled = true
@@ -17,7 +17,7 @@ singularity {
     // Use existing images from the centralized library, if available
     libraryDir = "/biocorelab/BIX/resources/singularity/images/"
     // Download images that are missing from the library to user space
-    cacheDir = "/ibex/user/$USER/.singularity/nf_images/"
+    cacheDir = "/ibex/user/${System.getenv('USER')}/.singularity/nf_images/"
 }
 
 process {

conf/mpcdf.config

@@ -4,6 +4,10 @@ params {
     config_profile_url         = 'https://www.mpcdf.mpg.de/services/supercomputing'
 }
 
+validation {
+    ignoreParams = ['max_cpus', 'max_memory', 'max_time']
+}
+
 profiles {
 
     raven {